I have microbial networks for more than 2 groups(6). I want to analysis the community structure and network properties among these networks all at the same time. Any web based or R-based tools would be helpful to me. Additionally I am also looking forward for tools that can be used to analyze the longitudinal nature of microbiome data and provide the networks or other attributes of microbiome. Any help and suggestions are welcome. Thanks
Hi Amit, while maybe not quite what you are looking for, I would direct you to have a look at the publications linked one of my PhD supervisors Dr. Umer Z. Ijaz (University of Glasgow) as the publications he has been involved in might help you find R script for your analysis. He has a website and also has some R script on Github you can access. One of his more recent works with Dr.Keating investigated networks in cod guts which may be of particular use. Article Drivers of ecological assembly in the hindgut of Atlantic Co...
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What kind of networks are we talking about here? Trophic networks? Co-occurence networks based upon "enterotype" (overal composition)?. What kind of samples are we talking about here? How many samples do you have to work with? With high numbers there are some nice yet simple visualisation tricks available to properly highlight such clusters/networks.
Marcus C de Goffau Here we are talking about the compositional network or the correlation based network for metagenomic sequenining in mouse. 6 animals per group are present. I am able to construct networks from each of the 4 groups based on different web based tool but next thing which i am looking forward is to compare these 4 group networks at once and not two at a time. Also, for the second part of my question is about the 16s data for 25 samples belonging to 4 groups collected over a period of 6 time points. I want to create a composite network for each group taking care of all the time points together and then compare these 4 networks within themselves. Hope this makes both the questions clear. let me know if you have any suggestions. thanks.
Talking about network comparison, you can opt for different topological comparisons network the groups.
R has lots of packages for that.
Cytoscape is also an option.
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